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saezlab / Omnipath_Cytoscape

a plug-in to access Omnipath from Cytoscape
http://apps.cytoscape.org/apps/omnipath
GNU General Public License v3.0
7 stars 0 forks source link

Update SendQueryTask.java #1

Closed gabora closed 5 years ago

gabora commented 5 years ago

fixing issue: permission denied to create file by Cytoscape plugin (@deeenes ) https://github.com/saezlab/pypath/issues/67

found this on Stackoverflow: https://stackoverflow.com/questions/14845045/permission-denied-when-writing-file-to-default-temp-directory possible problem: tmp folder returned by java.io.tmpdir is /tmp without the "/" in the end

gabora commented 5 years ago

Hey @cecca46, could you check the mentioned issue and if you think this could solve the problem? thanks

cecca46 commented 5 years ago

hello Attila,

sorry for taking so long to get back to you. I was unable to reproduce the error, which probably occurs on Linux machines only. I changed the code as suggested in that post and hopefully it will function on Linux machines too now. I could not test it however so please let me know whether that worked out.

From: Attila Gabor notifications@github.com Sent: 20 December 2018 14:27 To: saezlab/Omnipath_Cytoscape Cc: Francesco Ceccarelli; Mention Subject: Re: [saezlab/Omnipath_Cytoscape] Update SendQueryTask.java (#1)

Hey @cecca46https://github.com/cecca46, could you check the mentioned issue and if you think this could solve the problem? thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/saezlab/Omnipath_Cytoscape/pull/1#issuecomment-448999085, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVZzeWPiu38nWErxePu_yfJA8a--mzKhks5u65AugaJpZM4ZcMEZ.

gabora commented 5 years ago

Hi @cecca46 thanks for the update, could you please regenerate the target jar file too?

gabora commented 5 years ago

Hey @cecca46 I asked @Nic-Nic and he was able to reproduce the bug on his machine. Once you could make the .jar file he can test that too.

cecca46 commented 5 years ago

The .jar is updated. Please let me know whether it is fine.

From: Attila Gabor notifications@github.com Sent: 11 January 2019 14:45 To: saezlab/Omnipath_Cytoscape Cc: Francesco Ceccarelli; Mention Subject: Re: [saezlab/Omnipath_Cytoscape] Update SendQueryTask.java (#1)

Hey @cecca46https://github.com/cecca46 I asked @Nic-Nichttps://github.com/Nic-Nic and he was able to reproduce the bug on his machine. Once you could make the .jar file he can test that too.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/saezlab/Omnipath_Cytoscape/pull/1#issuecomment-453520848, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVZzeWTjeKWcvhs49NKjA9SXv3DOrga-ks5vCJVdgaJpZM4ZcMEZ.

gabora commented 5 years ago

Thanks @cecca46 , @Nic-Nic already tried the new version and it is working fine!!! I will update the jar file in the app store

best, Attila

gabora commented 5 years ago

Damn, the app store does not let me upload, because the version number must be increased. Renaming the file to Omnipath 1.1 was not enough. Could you please recompile it with a version number 1.1 ? thanks! @cecca46

cecca46 commented 5 years ago

the target dir now contains a new recompiled .jar file with updated pom file of version 1.1. Does uploading that one works?

From: Attila Gabor notifications@github.com Sent: 11 January 2019 15:18 To: saezlab/Omnipath_Cytoscape Cc: Francesco Ceccarelli; Mention Subject: Re: [saezlab/Omnipath_Cytoscape] Update SendQueryTask.java (#1)

Damn, the app store does not let me upload, because the version number must be increased. Renaming the file to Omnipath 1.1 was not enough. Could you please recompile it with a version number 1.1 ? thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/saezlab/Omnipath_Cytoscape/pull/1#issuecomment-453530688, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVZzebHDrrJXKFkSMXhKwm7CjnXhe6eKks5vCJ1IgaJpZM4ZcMEZ.

gabora commented 5 years ago

yep it works. http://apps.cytoscape.org/apps/omnipath

you are famous! 273 downloads.

deeenes commented 5 years ago

fantastic, thank you guys for managing this! :)

Nic-Nic commented 5 years ago

Should consider also updating the version/release tag on GitHub. I could do it on Monday